Analytical Report
SS200000464BL_C4
Alerts
  • Summary
  • Square Bin
  • Cell Bin
  • Image
Spatial Gene Expression Distribution
Spatial gene expression distribution plot shows MID count at each spot (bin200)
Tissue Plot with Spot (bin200) Colored by MID Count
1,017,675,955
Total Reads
22,463
Mean MID per Bin200
4,017
Mean Gene Type per Bin200
80,653,687
Unique Reads
Key Metrices
Total Reads
Total number of sequenced reads
Valid CID Reads
Number of reads with CIDs matching the mask file and with MIDs passing QC
Invalid CID Reads
Number of reads with CIDs that cannot be matched with the mask file
Discarded MID Reads
Number of reads with MID that have been discarded since MID sequence quality does not satisfy with further analysis
Clean Reads
Number of Valid CID Reads that have passed QC
Non-Relevant Short Reads
Number of non-relevant short reads
Uniquely Mapped Reads
Number of reads that mapped uniquely to the reference genome
Multi-Mapped Reads
Number of reads that mapped more than one time on the genome
Unmapped Reads
Number of reads that cannot be mapped to the reference genome
Transcriptome
Number of reads that are aligned to transcripts of at least one gene
Unannotated Reads
Number of reads that cannot be aligned to transcript of one gene (intergenic)
Unique Reads
Number of reads in Transcriptome that have been corrected by MAPQ and deduplicated
Sequencing Saturation
Number of reads in Transcriptome that have been corrected by MAPQ with duplicated MID
Total Reads
100%
1,017,675,955
Valid CID Reads
80.2%
816,520,301
Clean Reads
88.5%
722,584,742
Uniquely Mapped Reads
69.7%
503,971,957
Transcriptome
82.8%
417,255,267
Unique Reads
19.3%
80,653,687
Sequencing Saturation
80.7%
336,601,580
Unannotated Reads
17.2%
86,716,690
Multi-Mapped Reads
23.9%
172,441,738
Unmapped Reads
6.4%
46,171,047
Non-Relevant Short Reads
11.5%
93,935,559
Invalid CID Reads
16.0%
163,273,641
Discarded MID Reads
3.7%
37,882,013
Information
Sequencing
Total Reads
Total number of sequenced reads
Total Q30
Ratio of bases with quality value exceeded 30 in the sequenced reads
CID Q30
Ratio of CID (Coordinate ID) bases with quality value exceeded 30
MID Q30
Ratio of MID (Molecule ID) bases with quality value exceeded 30
Total Reads
1,017,675,955
Total Q30
86.46%
CID Q30
86.24%
MID Q30
80.33%
Annotation
Exonic
Number of reads that mapped uniquely to an exonic region and on the same strand of the genome
Intronic
Number of reads that mapped uniquely to an intronic region and on the same strand of the genome
Intergenic
Number of reads that mapped uniquely to an intergenic region and on the same strand of the genome
Transcriptome
Number of reads that mapped to a unique gene in the transcriptome. These reads are considered for MID counting. (Transcriptome = Exonic + Intronic)
Antisense
Number of reads mapped to the transcriptome but on the opposite strand of their annotated gene
Exonic
389,610,986
Intronic
27,644,281
Intergenic
86,716,690
Transcriptome
417,255,267
Antisense
100,281,607
RNA Mapping
Clean Reads
Number of Valid CID Reads that have passed QC
Uniquely Mapped Reads
Number of reads that mapped uniquely to the reference genome
Multi-Mapped Reads
Number of reads that mapped more than one time on the genome
Unmapped Reads
Number of reads that cannot be mapped to the reference genome
Clean Reads
722,584,742
Uniquely Mapped Reads
503,971,957
Multi-Mapped Reads
172,441,738
Unmapped Reads
46,171,047
Tissue Segmentation
Tissue
DNB Under Tissue
Number of DNBs under tissue coverage region
mRNA-Captured DNBs Under Tissue
Number of DNBs under tissue that have captured mRNA
Genes Under Tissue
Number of detected gene under tissue coverage
Number of MID Under Tissue Coverage
Number of MID under tissue coverage
Fraction MID in Spots Under Tissue
Fraction of MID under tissue over total unique reads (MID Under Tissue / Unique Reads)
Reads Under Tissue
Number of reads with position prior to filtration under tissue coverage
Fraction Reads in Spots Under Tissue
Fraction of mapped reads under tissue over total mapped reads (Mapped Reads in Spots Under Tissue / (Valid CID Reads + Discarded MID Reads))
DNB Under Tissue
91,521,240
mRNA-Captured DNBs Under Tissue
26,830,180
Genes Under Tissue
23,878
Number of MID Under Tissue Coverage
57,797,503
Fraction MID in Spots Under Tissue
71.66%
Reads Under Tissue
596,208,809
Fraction Reads in Spots Under Tissue
69.78%
Sequencing Saturation
(left) Plot of the sequencing saturation as a function of sequencing depth(bin200)
(middle) Plot of the median number of genes detected per bin as a function of sequencing depth(bin200)
(right) Plot of the unique reads detected per bin as a function of sequencing depth(bin200)
Tissue Square Bin Statistics
Bin Size
The size of Bin which is the unit of aggregated DNBs in a squared region (i.e. Bin 50 = 50 * 50 DNBs)
Mean Reads (per bin)
Mean number of sequenced reads divided by the number of bins under tissue coverage
Median Reads (per bin)
Median number of sequenced reads divided by the number of bins under tissue coverage (pick the middle value after sorting)
Mean Gene Type (per bin)
Mean number of unique gene types divided by the number of bins under tissue coverage
Median Gene Type (per bin)
Median number of unique gene types divided by the number of bins under tissue coverage
Mean MID (per bin)
Mean number of MIDs divided by the number of bins under tissue coverage
Median MID (per bin)
Median number of MIDs divided by the number of bins under tissue coverage
Bin Size
Mean Reads
(per bin)
Median Reads
(per bin)
Mean Gene Type
(per bin)
Median Gene Type
(per bin)
Mean MID
(per bin)
Median MID
(per bin)
1
13.86
5
1.51
1
2.15
2
20
2,574
2,509
135
135
249
244
50
15,778
16,145
612
633
1,529
1,544
100
61,275
63,978
1,714
1,823
5,940
6,093
150
133,619
141,655
2,894
3,143
12,959
13,409
200
231,717
248,944
4,017
4,433
22,463
23,597
Bin 20
(left) Scatter plot of MID count and gene types in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin
(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis
Bin 50
(left) Scatter plot of MID count and gene types in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin
(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis
Bin 100
(left) Scatter plot of MID count and gene types in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin
(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis
Bin 150
(left) Scatter plot of MID count and gene types in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin
(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis
Bin 200
(left) Scatter plot of MID count and gene types in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin
(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis
Clustering
(left) Clustering spots (bin200) under tissue covered with the Leiden algorithm
(right) UMAP projections of spots (bin200) colored by automated clustering. Same color is assigned to spots that are within shorter distance and with similar gene expression profile
Tissue Plot with Spots (bin200)
UMAP Projection of Spots (bin200)
Cell Bin Statistics
Cell Count
Number of cells
Mean/Median Cell Area
Mean/Median cell area (pixel)
Mean/Median DNB Count
Mean/Median number of DNBs that have captured-mRNAs per cell
Mean/Median Gene Type
Mean/Median gene types per cell
Mean/Median MID
Mean/Median MID count per cell
Cell Count
65,293
Mean Cell Area
221
Median Cell Area
195
Mean DNB Count
107
Median DNB Count
91
Mean Gene Type
88.17
Median Gene Type
78
Mean MID
155
Median MID
131
Cell Bin
(left) Scatter plot of MID count and gene types in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin
(bottom) Univariate distribution of MID count, gene types, DNB numbers, and cell area (pixel) with rug along the x axis
Clustering
(left) Clustering spots (cell bin) under tissue covered region with the Leiden algorithm
(right) UMAP projections of spots (cell bin) colored by automated clustering. Spots in the short distance are assigned with the same color have similar gene expression profile.
Tissue Plot with Spots (cell bin)
UMAP Projection of Spots (cellbin)
Image Information
Manufacture
motic
Model
MoticamProS5 Lite M
Scan Time
2022-3-7 16:10:25
Overlap
0.1
Exposure Time (ms)
8.139
Scan Rows
12
Scan Columns
10
FOV Height
2,036
FOV Width
2,436
Stain Type
ssDNA
Stitched Image
No
Image Name
SS200000464BL_C4_SC_20230423_121322_2.0.1
Stitching
Template Source Row No.
The row number of the template FOV used for predicting the entire template
Template Source Column No.
The column number of the template FOV used for predicting the entire template
Global Height
Height of the stitched image
Global Width
Width of the stitched image
Template Source Row No.
9
Template Source Column No.
2
Global Height
22,199
Global Width
22,173
QC
ImageQC version
ImageQC version
QC Pass
Whether the image(s) passed imageQC quality check
Track Line Score
Reference score for track line detection
Clarity Score
Reference score for image clarity
Good FOV Count
Number of FOVs that have at least one track dot detected
Total FOV Count
Total number of FOVs
Stitching Score
Reference score for stitching
Tissue Segmentation Score
Reference score for tissue segmentation
Registration Score
Reference score for auto-aligning image with gene expression matrix
ImageQC Version
2.0.1
QC Pass
Pass
Track Line Score
78
Clarity Score
83
Good FOV Count
103
Total FOV Count
120
Stitching Score
65
Tissue Segmentation Score
100
Registration Score
99
Registration
ScaleX
The lateral scaling between image and template
ScaleY
The longitudinal scaling between image and template
Rotation
The rotation angle of the image relative to the template
Flip
Whether the image is flipped horizontally
Image X Offset
Offset between image and matrix in x direction
Image Y Offset
Offset between image and matrix in y direction
Counter Clockwise Rotation
Counter clockwise rotation angle
Manual ScaleX
The lateral scaling based on image center (manual-registration)
Manual ScaleY
The longitudinal scaling based on image center (manual-registration)
Manual Rotation
The rotation angle based on image center (manual-registration)
Matrix X Start
Gene expression matrix offset in x direction by DNB numbers
Matrix Y Start
Gene expression matrix offset in y direction by DNB numbers
Matrix Height
Gene expression matrix height
Matrix Width
Gene expression matrix width
ScaleX
1.003
ScaleY
1.003
Rotation
0.629
Flip
True
Image X Offset
3,579
Image Y Offset
3,307
Manual ScaleX
-
Manual ScaleY
-
Manual Rotation
-
Counter Clockwise Rotation
90
Matrix X Offset
3.00
Matrix Y Offset
11.00
Matrix Height
26,457
Matrix Width
26,449
Horizontal Image Stitching Deviation Heatmap
Image stitching deviation in the horizontal axis, a lighter color indicates better stitching (the heatmap and frame of axes have been adjusted with the registration parameters)
Vertical Image Stitching Deviation Heatmap
Image stitching deviation in the vertical axis, a lighter color indicates better stitching (the heatmap and frame of axes have been adjusted with the registration parameters)